University of Otago, Gardner BinfLab

All

32 repositories

TIsigner_paper_2019
Public
Code related to TIsigner manuscript and webserver
bioinformatics structural-biology multiprocessing protein rna-structure simulated-annealing translation-initiation-site biotechnology
Jupyter Notebook
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Other
•0•1•0•0•Updated Nov 16, 2024Nov 16, 2024
Avoidance-v2
Public
Jupyter Notebook
•0•0•0•1•Updated Jun 17, 2024Jun 17, 2024
Enterobacteriaceae-TraDIS
Public
Gnuplot
•0•0•0•0•Updated Jun 11, 2024Jun 11, 2024
PCPBFull
Public
A software pipeline to reproduce results in the paper 'Flawed machine-learning confounds coding sequence annotation' by the Gardner Lab
Shell
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MIT License
•0•0•0•0•Updated Jun 9, 2024Jun 9, 2024
PCPBSlim
Public
Data and results for the paper "Flawed machine-learning confounds coding sequence annotation"
Shell
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MIT License
•0•0•0•0•Updated Jun 9, 2024Jun 9, 2024
invasive_salmonella
Public
Data and code to accompany our paper on identifying patterns of gene degradation associated with invasiveness in Salmonella
Perl
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GNU General Public License v3.0
•1•7•0•0•Updated Apr 26, 2023Apr 26, 2023
TISIGNER-ReactJS
Public
TISIGNER: Unleash the power of synthetic biology
structural-biology webserver synthetic-biology multiprocessing protein solubility rna-structure simulated-annealing translation-initiation-site biotechnology
JavaScript
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Other
•7•18•0•12•Updated Mar 3, 2023Mar 3, 2023
PPI_Analysis_2022
Public
An accurate, scalable and generalisable tool for predicting protein-protein interactions
Python
•0•1•1•0•Updated Nov 4, 2022Nov 4, 2022
Razor_paper_2021
Public
Jupyter Notebook
•0•0•0•1•Updated Oct 27, 2022Oct 27, 2022
TIsigner
Public
Translation Initiation coding region designer
bioinformatics structural-biology webserver multiprocessing protein rna-structure simulated-annealing translation-initiation-site biotechnology
CSS
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Other
•3•2•0•3•Updated Jun 21, 2022Jun 21, 2022
speed-vs-accuracy-meta-analysis
Public
scripts and datasets associated with a study of benchmarks of bioinformatic software
TeX
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Other
•3•3•0•0•Updated Jan 21, 2022Jan 21, 2022
genome-randomisation-survey
Public
A survey of methods for randomising genome sequences
Perl
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Creative Commons Zero v1.0 Universal
•0•0•0•0•Updated Dec 22, 2021Dec 22, 2021
thesis-bikash
Public
Final version uwu 😊
latex
Jupyter Notebook
•0•0•0•0•Updated Nov 2, 2021Nov 2, 2021
Streptococcus-pyogenes
Public
Streptococcus pyogenes
Jupyter Notebook
•0•0•0•0•Updated Aug 20, 2021Aug 20, 2021
deltaBS
Public
Quantifying the significance of genetic variation using probabilistic profile-based methods.
TeX
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MIT License
•1•17•1•0•Updated Apr 21, 2021Apr 21, 2021
Razor
Public
Tool to predict eukaryotic signal peptides. In addition, prediction of toxin and fungi signal peptides is also done.
fungi cleavage-sites signal-peptide toxic-proteins
Python
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Other
•1•4•1•0•Updated Feb 22, 2021Feb 22, 2021
SoDoPE_paper_2020
Public
Jupyter Notebook
•5•9•0•0•Updated Jan 2, 2021Jan 2, 2021
ncVarDB
Public
Repo for the ncVAR database
R
•2•2•0•0•Updated Oct 13, 2020Oct 13, 2020
Non-codingDBS
Public
A repository to keep files for Delta-bitscore non-coding variation project.
Python
•0•0•0•0•Updated Jun 15, 2020Jun 15, 2020
Compartmentalisation_Marsden2019
Public
R
•0•1•0•0•Updated Apr 3, 2020Apr 3, 2020
EnTrI
Public
0•0•0•0•Updated Mar 13, 2020Mar 13, 2020
beth-thesis
Public
Gnuplot
•1•0•0•1•Updated Feb 27, 2020Feb 27, 2020
uniqueome2
Public
0•0•0•0•Updated Nov 27, 2019Nov 27, 2019
robustness-RNP
Public
A series of comparisons of the mutational robustness of RNAs and proteins.
HTML
•1•0•0•0•Updated Nov 14, 2019Nov 14, 2019
twilight_zone
Public
Manuscript, code, important data
Perl
•1•0•0•0•Updated May 8, 2019May 8, 2019
RNA_Interactions_Benchmark
Public
RNA-RNA interaction predictions tools benchmark scripts, wrappers and datafiles.
Python
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MIT License
•1•7•1•0•Updated Feb 28, 2019Feb 28, 2019
invasive_campylobacter
Public
Data and code to accompany our work on invasive Campylobacter isolates
Perl
•0•2•0•0•Updated Dec 11, 2018Dec 11, 2018
meta-analysis-eDNA-software
Public
A meta-analysis of environmental DNA sequence analysis benchmarks
R
•0•0•0•0•Updated Oct 15, 2018Oct 15, 2018
sRNA_evo
Public
Beths sRNA evolution project, and other scripts
Perl
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GNU General Public License v3.0
•0•0•0•0•Updated Sep 26, 2018Sep 26, 2018
Avoidance
Public
RNA avoidance scripts and data.
R
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MIT License
•2•1•0•0•Updated Mar 7, 2018Mar 7, 2018